Like always "divide and conquer." In a big program, I identify "subprograms" that can have only the "interface" (the very limited set of structures and functions) exposed to the rest. The subprograms aren't "libraries" in a sense that I do much faster changes to the "interface" but just having them makes everything much more maintainable. So some headers are visible only inside of the "subprogram." Second: not everything is worth to appear in headers at all: I use the functions and declarations local to the compilation unit as much as I can.

Back to the main topic, using structures properly will result in the best code you can produce for anything not trivially small. Practically every CPU I know of is specifically optimized to make addressing elements in the C structure as efficient as possible.

In your case, if there are a lot of functions to which you pass the pointer to the structure, then if you take care of the organization it means that they really do have to operate on the structure. But if you have a lot of arguments to any function, you probably need some even bigger structure and pass that around.